AW: script for equilibration

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Oct 04 2011 - 00:18:04 CDT

Hi,

no, that won't minimize as the last task. Try with minimize as last command. If that doesn't work, just write another script for the minimization and use the restart files from the run before.

Good luck

Norman Geist.

-----Urspr√ľngliche Nachricht-----
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von matziast_at_med.uth.gr
Gesendet: Sonntag, 2. Oktober 2011 11:19
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: script for equilibration

Hi,
I need your help. In the following script I want to ask you this: the last
command is minimize. Does this minimization follow the equilibration? Because I
would like to run after equilibration, a minimization. Is it the right script?
I would appreciate if anyone could help me.
Thank you in advance,
Maria.

#########################################
### JOB DESCRIPTION
#########################################
# Equilibration of run.coor
##############################################

## ADJUSTABLE PARAMETERS
##############################################

structure run.psf
coordinates run.pdb
#bincoordinates eq1.1.coor
set temperature 300
set outputname eq
firsttimestep 0

##############################################
## SIMULATION PARAMETERS
##############################################

# Input
paraTypeCharmm on
parameters run.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 # 2fs/step
rigidBonds all # needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
#dielectric 80 ##########23/11/2010
stepspercycle 10
# Constant Temperature Control
langevin on # do langevin dynamics
langevinDamping 5 # damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off # don't couple langevin bath to hydrogens
# Output
outputName $outputname
restartfreq 500 # 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100

###########################################
## EXTRA PARAMETERS
###########################################

# Spherical boundary conditions
#sphericalBC on
#sphericalBCcenter 22.04675205 62.204443 16.8283
#sphericalBCr1 62.5 # distance at which the first boundary potential begins to
act
#sphericalBCk1 10 # force constant for the harmonic bountary potential
#sphericalBCexp1 2

# Constraints and restraints
#fixedAtoms on
#fixedAtomsForces on
#fixedAtomsFile Y-0.ref
#fixedAtomsCol B
##########################################
## EXECUTION SCRIPT
##########################################

# Minimization
minimize 250
reinitvels $temperature;

run 500000; # 1 ns

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:52 CST